First, I think I'd put a vacuum gauge on there and see what you can see. Get some numbers.
Second, advance the initial timing if you have to, and see if you can get the vacuum up (if you need to), then you can adjust total to make up for it. You have a stout starter, but if not, you could even start it airplane style by hitting your button, then turning on the ignition.
Third, call FAST and see if it is possible to run in open loop at idle. What this will do is essentially make the TBs an electronic carburetor and not require (or adjust for) any inputs, however, you will have to screw with settings because you lose the "learn" feature for idle when you do that. Additionally, many of us use open loop for initial tip-in to make up for a bunch of overlap, then after a desired RPM, it goes into closed loop, same at cruise
Fourth, you could add a little valve lash (never did a SOHC, so not sure if it's possible) but it should be feasible, that may bring you a little more vacuum, although that doesn't bring much.
Finally, Jay can say more on what the chance of this is, but if you advanced the cams, you can likely gain significant vacuum at dile, but not sure how easy that is on an aftermarket SOHC
However, in the end I am quite surprised that it would need more vacuum than you have. Somehow, you likely just need to get into the system and tell it what it needs to know. I know you spent dough on this new handheld, but you possibly could be getting into the realm of laptop tuning. That's why I like a laptop so much better, I can long, tweak, sit at my computer think about it, try something and basically hit undo and redo 50 times a day if I wanted to
ON EDIT: I spent a very short time with the EZ-EFI instructions, and some questions
1 - Are you using it to control the ignition?
2 - There is quite a bit of tuning capability, but moreover, there is a ton of calibration capability. TPS, IAC, etc, Have you done all of those? We know you know of the TPS, but I saw a page that calibrated the IAC and throttle plates, that triggered my question.
3 - Just to clarify, do you think that your brake booster is bleeding vacuum when sitting there at cold start? It shouldn't
Get a vacuum gauge on there, see what it says, this may be a moot point. However, if it's only slightly low, adding a little initial and adjusting back to total may put your mind at ease.